Mechanisms are what is discovered in much of science, especially in molecular biology. This work proposes a new analysis of the concept of a mechanism, which includes the activities of mechanisms, as well as their component parts. Types of activities important in molecular biology are geometrico-mechanical, e.g. an inducer fitting into a groove of a repressor protein and changing its shape; electro-chemical, such as covalent bonding between amino acids or hydrogen bonding between nuclei acid bases; and energetic, such as active consumption of ATP or passive diffusion across a membrane. When mechanisms are proposed, the scientist must specify the activities, as well as the components parts, the set-up conditions, a continuous transition of steps, and the termination conditions, such as the production of a product.
Questions to be addressed are the following: How are mechanisms represented? How are mechanisms discovered, evaluated, and revised? What reasoning strategies are sufficient for mechanism discovery, evaluation, and revision? What experimental strategies are used for testing hypothesized mechanisms?
The primary case study to be examined is the mechanism of protein synthesis represented by the "central dogma" of molecular biology in the period from 1953 until about 1970 (plus some anomalies still problematic). The mechanism's historical development through cycles of discovery, evaluation, and revision illustrates the process of anomaly-driven mechanism redesign, one of several important reasoning processes in contemporary molecular biology.
This work thus contributes to the questions in philosophy of science about the nature of theory structure in molecular biology -- a set of mechanisms-and the reasoning in scientific change--reasoning strategies for discovering, evaluating, and improving mechanisms.
